In Our Minds
by leigh.m5576
Summary: Years in the future, Clary tells the story of her life. With Jonathan on the loose, the Shadowhunters don't have much time to deal with anything other than his imprisonment. But when deaths begin to plague the institute, they can not ignore this new peril. Jace and Clary struggle through death and misery, but their arms are always there to hold onto each other-
1. Chapter 1

**Hey guys! Another story wooooooooooo. OK so this time is different…. IM ACTUALLY GOING TO FINISH THIS ONE! Honestly *sighs* so far I haven't really committed to my stories (don't read them they suck and I never continued them), so this time I make a promise… this story is not going to fail after one chapter… because I've already written 3! Yaya. Anyways please R&R because I love it xx and don't forget that I am aussi e so sorry for any strange material you come across… just ask and I will explain **** have fun xx**

**Disclaimer: I don't own any characters or previous plot… that all goes to Cassandra Clare :/**

**Love ya xx**

**Prologue**

_-6 years after the events of City of Lost Souls-_

Have you ever looked back on yourself, and laughed at how completely ignorant you must have been? Seen your own smiling face and turned away in disgust.

Longed for times so much simpler than the ones you live in right now.

I have. Every day.

I can still see those days in my past, burned into my mind like I lived them over. I might as well have. I see them in my sleep every night.

After a bad night I find refuge in places that I always knew I would. Years ago, before any of this happened; I would lie in the arms of a golden haired boy.

To this day, I still do. He is my light. My everything. That never changed.

Everything around me did though.

I am Clarissa Fray.

And there is a lot I am going to tell you.

**Chapter 1**

The crowds of people bustling through New York took no notice of a small redheaded girl cradling an injured arm, as she tried to avoid bumping anyone and inflicting pain. Agitated, Clary decided to give up on walking back to the institute, and pushed her way into an alley so she could make a portal without anyone gaping behind her as she left.

It had been a long day. Clary had awoken early and left for the Institute so she could continue in her Shadowhunter training. With the threat of Jonathan, her psychopath brother, looming like a black cloud over her friends and family, her training had never been taken more seriously.

After an intense session of agility tests with Maryse, Clary had retired to Jace's room and the couple had spent some time just doing normal teenage things. Clary almost felt calm.

That was until Jace was called on by Isabelle to discuss battle plans, in which Clary tagged along. She tried to be as helpful as she could, but found nothing to say, and so Clary did the honourable thing by offering to get everyone coffee from Starbucks.

Now here she was, wincing in pain as she pulled her steele out from her coat, after being crushed against a wall in a brawl with a particularly large and ugly demon. In the end, Clary had come out victorious, but she had landed what was probably a broken collar bone. Even after tracing multiple _iratzes_, it still hurt like a bitch.

Finally, Clary managed to hastily draw a portal and step through inside the institute walls. Grumbling about the cold, it was around mid-November, and cradling her injured arm, Clary sought out Jace who would undoubtedly help her with anything she wanted after being injured on a coffee run. It was exactly what she needed.

As expected, Jace was outraged to know that Clary had to fight off a demon by herself with minimal training. But he calmed down after Clary assured him she was fine, and had only banged up her collar bone a bit. He frowned at that.

"Let me see then" he remarked. Jace helped Clary out of her heavy coat, making a note to raise an eyebrow when she winced. "Just banged it up huh" he smirked. After Jace made her some tea to warm up, Clary cuddled down into his chest.

Isabelle, Alec, her and Jace were all gathered around the table near the kitchen. Isabelle made a face at Jace and Clary, obviously disapproving of their position; Clary sitting on Jace's lap, her head tucked under his chin. She was still holding her arm where her collar bone throbbed, but was comfortable in her boyfriend's arms.

The night went slowly after that. Not having much to do, the Shadowhunters lounged around; not a common thing for someone like Jace, who liked to be up and moving at all times. So Clary let herself relax and found her mind wandering to scenarios where none of her new life existed. What if she had never bumped into Jace in that club that night?

_Stop_. She was better off now. Wasn't she? Clary sighed. She couldn't deny that her Shadowhunter life had been hard. Especially the part where her biological father and brother had both turned out like they had. _Murderers and worse. _

It wasn't something she liked to think about, but it always seemed to be on her mind, seeping through the cracks of the walls Clary had built after she escaped him. At night, when she was laying in the darkness, images would haunt her thoughts, plaguing Clary with fears and nightmares.

Most nights ,and these were always the best nights, Jace would find Clary screaming and his arms would comfort her in the darkness. Together, they would fight the mark Jonathan had left on them both.

She tried to remind herself that she had to be strong, but with the darkness of the night, it was hard to hold on to happy memories. She would be trapped in a haze of dreams and horror where her brother was always haunting her.

_His_ voice would ring through her head. _We are alike, you and I,_ he would say. _You are my sister, and you belong to me only. _

Clary woke with a start.

"Jace, I'm going out with Izzy!" Clary called through the echoing walls of the Institutes training room. She sighed when no answer came.

Jace was currently training, and as Clary had come to learn, this meant it was not a good time to be a pestering girlfriend. She would have to find ways to entertain herself for the time being, and so she had planned a night out with Isabelle.

"Jace?" Clary called again, losing patience. Crossing and uncrossing her arms for the third time, she gave up. "Let's just go Izzy". Her voice was clearly pissed off.

Izzy looked at her friend with her eyebrows raised. "You sure? I'm not ever really going to be in the mood to deal with 'protective boyfriend' Jace" Isabelle snorted. Clary picked up her car keys off a table in the hall and headed for the door, her hair swinging loose behind her. "Definitely. I really need some girl time anyway."

Izzy grinned. "Thank god. I was hoping for some dirt on Jace. It's in a girl's nature to do some bitching once in a while anyway."

Clary grinned.

**Thanks for reading! Ok so for this story, reviews on how the story goes will be welcome, all though keep in mind that I had to plan for it to go somewhere. **

**This is not just another one of those City of Heavenly Fire fanfics-as you will find out later… **

**Please keep reading cause I love ya!**

**xxxxxxx**


	2. Chapter 2

**Ok so here is chapter 2- hope you like it!**

**-warning! If you hate tragic things- then don't read. I'm sorry everyone, but what you read now is vital to the plot… don't hate me… **

Chapter 2

Clary was on edge the whole night. The girls had a great time, but hidden in every laugh about protective boyfriends, was a nagging feeling that something wasn't right. Clary could feel Goosebumps prickle her skin in the cold night air.

"This way" Izzy urged. After having a slow meal at some small Italian restaurant, Isabelle had insisted that their night was not over. "I can't stand to be at that Institute for a minute longer. It's so sad, I swear Alec's break up vibes are ruining my mojo."

Clary snorted, and almost tripped over a loose brick. Now Isabelle laughed. "I wonder if the Shadowhunter in you will ever come out."

"Believe me, I ask myself every day. Maybe I just wasn't cut out for this." Clary sighed. "In theory I could always just be Jace's trophy wife". Isabelle turned a sharp corner and the scent of burnt sugar wafted through the air.

Clary cocked her head as she caught on, looking around for danger. Nothing seemed out of the ordinary and Isabelle hadn't seemed to notice even with her _senses_ rune peeking through the sleeve of a halter top.

"Imagine that. 'Jace honey are you home? Dinners on the stove and your bath has been run'" Clary faked a posh housewife accent. The girls burst out laughing at the ridiculous statement, and walked into the night. "So you are going to marry Jace? Someday at least." Clary was flustered by Isabelle's question. Her tone had changed. It was distant and soft, all the humour gone.

"Yeah." Clary replied, surprised by her own answer. "Yes. Yes, I will someday" she said more confidently this time, smiling to herself. "Don't tell Jace though. A woman's got to keep their man on their feet". Something changed that night. Clary could feel it.

"Really?" Isabelle's voice rang through the halls of the institute. "Now… Ok I'll be right over" Clary crossed her legs and went back to the sketch she was working on. The walls were not thick, and sounds, especially annoying ones like Isabelle's phone conversations, seemed to echo through each room.

"Clary" Izzy called through the doors and walls. "Clary I'm going to Simon's house ok! Watch out for ass hole brothers and make sure you use protection!" Isabelle said with a smirk leaking into her words.

Clary's eyes widened as she quickly answered, "No problem bye!"

Ever since Jocelyn had reluctantly given in to her daughter staying at the institute, Clary had moved her things into one of the many identical rooms the old church held. It was as far as possible from Jace's room, thanks to her mom's careful planning, but much better than being in a different building.

Mainly, the reason this agreement was even permitted was because of Sebastian's previous break in. There was no way Jocelyn was letting Clary stay at the same house again. She would visit on weekends, but her contact with her mom had certainly lessened. Clary wasn't complaining.

_Especially because of this,_ Clary thought as she abandoned a half-finished drawing of the New York city scape and tip toed outside of her boyfriend's room. "Jace" she whispered through the wood door to his room.

"Come in" he replied, and Clary peeled the door open. He was sprawled over the starch white bed spread, reading a book that was balanced on his toned stomach. Clary grinned. She loved seeing him like this, relaxed and at ease. It made her feel warm to know he trusted her to become a part of his home.

He trusted her to see him when no one else would. The same went the other way as well. Clary quietly closed the door behind her before tip toeing over to his bed. Jace abandoned his warn out copy of some coverless book, and opened his arms.

They spent the night like that, wrapped in each other's arms, guarding them from the darkness that Jonathan brought. It was something Clary had grown used too, and she found it becoming a pattern of their nights.

She would sneak into his room, and he would be waiting for her to fold into his arms. "I wish it could be like this forever" he said some nights later.

"Really?" Clary turned her head to look at her boyfriend. "Running and hiding from my lunatic brother with the certainty that he will come back to steal us away and use us to take over the world?" Clary smirked. She loved making him smile.

But this time he didn't. Jace's face was distant and his flawless features were serious. "I mean right here, right now. When you're wrapped in my arms, I know nothing can hurt us. No matter what we go through, I want this to stay the same. You sleeping in my arms"

Jace shifted his body so he could hold her closer, and Clary melted into his warmth. "I know" was all she said and they drifted into sleep filled with dreams and thoughts of the future.

"Mom I'm here!" Clary called through her old house where her mother and Luke stayed. She checked the clock on the wall impatiently. It read quarter past eight.

Clary had been out all afternoon. With Robert, Maryse and Alec (who was still the only Shadowhunter of age) away on Clave business in Idris, Clary, Isbelle and Jace were left to the upkeep of the Institute.

And as Clary was learning, that was not an easy job. There were groceries to be bought (Isabelle insisted she take this duty) and weapons to be sharpened (Jace, of course had promptly announced he would be the one to do this) so Clary was left to run errands around New York.

Jace had insisted that Simon would accompany her, and neither her nor her best friend had protested. Sometimes it was nice to pretend they were normal high school kids. Clary enjoyed her time spent doing household activities with Simon.

But the day had bled out, and eventually it was time to return to her mom's house where she had promised to stay the night. Reluctantly promised.

"Mom?" Clary's voice echoed through the walls. A sick black feeling crept up into her stomach. This reminded her way to much of a time not too long ago when she had come home to find her mother had been taken.

"Mom!" Clary tried again, and was now searching each room of the house, for clues or anything. _Calm down Clary_, she told herself. She was probably just over reacting, but the nauseating feeling in her stomach didn't go away.

Clary kept searching until she reached the last room in the house. Jocylen and Luke's bedroom. The door was slightly cracked, Clary noticed as she padded slowly forwards, her heart beating in her ears.

Everything had gone slightly blurry, as if she were walking through a memory.

Sounds were echoing through her brain. A lawnmower somewhere in the distance. Clary's had was on the door knob. Car horns honking on the streets. Something in the door squeaked as it opened. People bustling through the city. The room came into focus.

Silence.

No sound at all. Everything was wrong.

Why was Jocylen laying still on the bed? Her red hair splayed around her face. What was the red liquid staining Luke's t-shirt?

Why were they so still? Too still. Silence flooded the room.

What.

Was.

Happening.

**KEEP READIN PEOPLE I PROMISE IT WILL GET BETTER- because this leaves the perfect op for fluff with Jace and Clary xx**

**Woooooo **


	3. Chapter 3

**CHAPTER 3 OMG… Ok this is actually so sad **** thanks to all the followers **** love ya, and here is the next chap up xx**

Chapter 3

Clary was lying at the bottom of a staircase, covered in blood when Jace found her.

She was sobbing quietly to herself. Jace's immediate thought was that she had been hurt. He called her name quietly and touched her as if touching a wounded animal. She started making sounds like she was one.

"Not me" she whispered into his ear. Jace scooped her up into his arms, cradling her like a baby. "I'm not hurt" Jace heard through Clary's harsh breathing. He looked up suddenly as a shout was heard from the room above the staircase. It was Isabelle.

The was no way anything would made Jace leave Clary now, as she sobbed into his arms, her tears staining his gear. "Mom" she whispered, and tragedy clicked into place. Jocylen? "Isabelle?" he called to his sister.

No answer.

"Isabelle!?" he said more urgently this time.

"Don't come up here with Clary!" she yelled back, her words cracking. "Take her back to the institute" her voice was clearer now. Determined to help her friend.

"I'm leaving, make sure you return safely". Jace tucked Clary's head into his chest, as his heart broke under her sobs.

They took a taxi back to the institute. Clary was leaning her head on Jace's shoulder, staring into endless space. They reached the large doors, and were let in almost immediately. Clary said nothing.

Jace led Clary up to his room, where he lay her down on the bed and changed out of gear. There was nothing he could to comfort her now. Jocelyn and Luke were dead. Murdered. And death meant there was no going back.

Jace heard a murmur from behind him and turned his head to see if Clary had spoken. "It was Jonathan" she whispered, louder this time. "We don't know yet Clary" he replied softly, but the rage in her eyes told him there was no convincing her.

A memory of the day Jace witnessed Valentine's death, or supposed death, ran in his mind. The grief that followed him around like a dark cloud that had only ever really left when Clary was there to make it. He remembered clearly how it felt to watch your parent die. It wasn't like anything else in the world.

"Clary, go to sleep" Jace said, defeated. He felt utterly hopeless, filled with longing and want. It was his responsibility to protect Clary from pain, and yet he was here, helpless and out of ways to comfort her. "I'll just see them in my dreams" she said, closing her eyes, as if she were wincing in pain.

Jace pulled up the covers of the bed, and crawled under, pulling Clary with him. "Just sleep" he insisted, and wrapped his arm around her. This was better. He could feel Clary's breathing slowing, and her eyes begin to droop as he stayed awake to fend of the nightmares to come.

He stroked her hair as she finally drifted of, and prayed, wished and hoped for refuge from the world filled with death.

In the morning, Isabelle had returned, and she pulled Jace away from a still sleeping Clary to discuss what had happened.

"Stabbed" she said. "In the stomach. It looks like they put up a hell of a fight though" Isabelle lowered her eyes to the floor. "They would have died at around eight am yesterday morning. I'll send word to the Clave in a few minutes." She trailed off and looked at Jace, whose hair was still ruffled from holding Clary and the bags under his eyes told Izzy he hadn't slept at all.

"Do you think it was… Sebastian?" her voice was a whisper.

"Honestly, yes" Jace replied. "But I don't think Clary should know that yet. I don't think Clary should know anything". Isabelle began walking to the kitchen, and Jace followed. When they reached the main room of the institute, they returned to discussing the inevitable.

"How is she?" Isabelle asked cautiously, whilst making coffee. Jace averted his eyes. "How do you think" was all he said. Isabelle shook her head. "She's been through so much already… I just don't understand why this had to happen."

Jace's face scrunched in disgust. "If Jonathan did this…" he trailed off, distracted by his own furious thoughts. "He should wish he was never born."

"But we aren't sure" Isabelle rebutted. "We don't know it was really him. The clave are going to investigate the scene in the next few days. It has been deemed of importance." She sighed. "Just why Clary, you know? Why her parents of anybody else? I mean, I'm not wishing this on anyone but, who decided it would be Clary who had to deal with being an orphan" Isabelle stopped her rant at the look of pure and furious rage on Jace's face.

"She shouldn't be going through this. I know what it's like" He said quietly, almost spitting the words out. "Go check on her. Make sure she's going to get through this, alright? You are all she has got left" Isabelle said.

"I know" Jace sighed, standing up in an ultimatum.

There was nothing left to do but wait for the pain to fade.

**KEEP READIN PLS xx**


	4. Chapter 4

**Heyo! I haven't updated in a while sorry it's the holidays so yeah. Enjoy the chapter xx**

Chapter 4

Clary was a wreck.

There was no doubting that. She didn't leave Jace's room for days, showering and eating there. Clary just couldn't face the world.

She tried so hard to stay strong. To uphold her Shadowhunter name, as they dealt with loss so much, but grief wouldn't release its grip on her. Jace was the only thing that made sense. He was always there to hold her and comfort her, even when Robert and Maryse had returned from Idris.

Jace had even stayed behind when Izzy, Alec and Jace's foster parents had gone to the Clave meeting about the murder of Jocelyn Fairchild and Lucian Garroway. Isabelle had returned with grim news.

"They think it was Jonathan" she said, looking pale and tired. Jace wasn't surprised. It was as he had suspected. "Was there any evidence?" he questioned. Isabelle pursed her lips. "Well, there was something pretty interesting near Jocelyn's body. They found an artefact belonging to a very old Shadowhunter family. It had their emblem on it"

Jace was confused. "I don't understand? Why whould they assume Jonathan had killed them when there was that next to a body?" Isabelle looked grim. "There was also a ring left behind. One they know belonged to Valentine. The clave think it was left on purpose. To send a message."

Jace frowned. "That doesn't add up."

"Exactly" Isabelle said. "That's why they can only assume it was Jonathan. They can't know for sure… but I think something weird is going on"

Just then Isabelle's eyes widened at something over Jace's shoulder. He turned quickly to find Clary leaning on the door frame to the library where they had been talking. "Hey" she said weakly. It was the first time she had been anywhere in days.

"Hi" Jace stood and walked over to his girlfriend. "How are you?" he asked, concerned. She ignored him. "How is everything going? Did they find proof that Jonathan did it?" Clary's voice was harsh. Isabelle shot a meaningful look at Jace who looked incredibly lost. "Ummm" Isabelle started, not really sure where to go.

"Cut the crap, I can handle it" Clary snapped. "I've sat around doing nothing for long enough. I want to help." Isabelle was just taken back by Clary's outburst. She was sort of relieved that some of Clary's fire was returning.

"Ok, so you're feeling better?" she ventured.

"Yes" was her answer. Jace was concerned. He knew better. "Clary, you can just sit tight for a little longer. The clave haven't come up with much. It's a bit of a…" Jace trailed off, unsure of how much to reveal. "Conundrum" he finished.

"Then tell me" Clary insisted. "I really just want to help. I need to know what happened" A pleading note had crept into her voice. The kind that was restless for revenge and knowing. Jace knew she wouldn't rest until whoever had ripped her mom from her life would pay the price. It was terrifying to think.

"Clary" Isabelle started, but was cut off with "Please! Tell me. I promise I can help".

"But…" Isabelle tried again. "No!" tears had started to leak from Clary's eyes. "Just tell me" she sobbed, and Jace grabber her arm, and Clary collapsed to the floor, her head falling into her arms. "I hate being so weak" she stated, through sharp breaths.

"I need to do something Jace!"- "Breathe Clary" Jace tried to calm her down. "Just breathe." Clary tried to follow his orders, but her erratic breathing never stopped.

She stayed like that, her knees puller to her chest, head in hands for a long time. Jace eventually sat next to her and wrapped her into his arms. This helped. Feeling safe and protected, in the embrace of the only person who could. It was familiar. Clary calmed down, but was left feeling empty inside.

Was she ever going to be ok?

Maryse Lightwood was listening half-heartedly to the droning voice of Clave members.

The meeting at hand had gone on for far too long, with far too little achieved. And she was sick of it.

"Jonathan Morgenstern is still a number one priority!" a stern voice rang out over the arguing. "All efforts should be placed in the way of his capture"

"Elijah please" another voice cut in, this time a woman's.

Maryse recognised her as Gabriella Stonefall, a moderately placed member of the Enclave in London. "This is petty. A Shadowhunter had been murdered. In cold blood. We have come to the conclusion that this was not an act of Jonathan Morgenstern, and so there is ultimately a new threat at hand"

"Gabriella is right" Sophia Penhallow declared. "We cannot afford to ignore a new problem. It will only grow larger." The hall was filled with Shadowhunters from across the wold, here to discuss the murder of Clary's parents.

Elijah Willhelm didn't stop. "No! This is a disgrace! Jonathan his killed many more Shadowhunters, of much higher placement in the Clave."

"If this is about importance in the Clave, then your views are tainted!" Sophia's voice rose.

"If we ignore this then Jonathan Morgenstern will not be our only issue." Maryse spoke up and silence spread through the gathering hall. Mayrse was known throughout the Shadowhunting community.

"No. We must be vigilant. Jonathan is still missing and plotting against Shadowhunters, so he cannot be ignored." She paused and saw a smug look on Elijah's face.

"But… with recent events we cannot afford to ignore, I believe investigation must be made into the murder of Jocelyn Fairchild and Lucian Garroway. Something that we don't understand is happening, and we must have the knowledge to make a logical judgment."

Maryse sat back in her seat. She could see nods and whispers of approval rippling through the crowd.

Vaughn Lanceworth was pacing the dungeon of his family's mansion. Something had gone terribly wrong.

His plan was ruined, because of a small mistake.

How could he have been so stupid! One, simple problem could be the downfall of this whole mission. One stupid piece of evidence. The old watch his grandfather had given him had been left at the scene.

Vaughn threw a petite vase of flowers at the wall in rage. He was not going to get the blame!

"Brother" he called into the darkness. "I will not be held responsible for this!", rage shook his voice. "I was not the murderer of Jocelyn Fairchild!"

**Keep reading guys xx**


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